A Graphene-Based Microfluidic Platform for Electrocrystallization and In Situ X-ray Diffraction

Microfluidic technologies for protein crystallography: advances and applications

Three-dimensional protein structure determination by X-ray crystallography is essential for understanding biological function and accelerating drug discovery. However, obtaining high-quality protein crystals remains a significant bottleneck. The conventional crystallization methods are often labor-intensive, require large sample volumes, and offer limited control over the crystallization environment. This review summarizes the application of microfluidic technologies to protein crystallography with a focus on their advantages over the conventional crystallization methods. Microfluidic devices enable nanoliter-scale sample handling, precise control over crystallization conditions, and high-throughput screening, addressing major limitations of the conventional approaches. This review introduces various microfluidic platforms, including droplet-based and microwell-based systems, for protein crystallization, crystal growth control, and on-chip X-ray diffraction analysis. The review also covers the use of microfluidics for creating diffusion-controlled crystal growth environments, real-time crystal growth measurement, on-chip X-ray diffraction measurement, and room-temperature X-ray crystallography with automated data processing.

Cyclic Olefin Copolymer-Based Fixed-Target Sample Delivery Device for Protein X-ray Crystallography

Serial macromolecular X-ray crystallography plays an important role in elucidating protein structures and consequently progressing the field of targeted therapeutics. The use of pulsed beams at different repetition frequencies requires the development of various sample-conserving injection strategies to minimize sample wastage between X-ray exposures. Fixed-target sample delivery methods that use solid support to hold the crystals in the X-ray beam path are gaining interest as a sample-conserving delivery system for X-ray crystallography with high crystal hit rates. Here, we present a novel fixed-target microfluidic system for delivering protein microcrystals to X-ray beams for diffraction data collection and structure determination. The fixed-target design consists of 3 symmetric sections arranged in an area of 1 in. × 1 in. with up to 18,000 crystal traps per device. Each trap is targeted to hold one crystal up to 50 μm in size in the largest dimension. The device has been fabricated using cyclic olefin copolymer (COC) for high-quality diffraction data collection with low background scattering induced through the fixed-target material. The newly developed fixed-target device is designed for vacuum compatibility which will enable the use in vacuum experimental chambers of X-ray radiation sources including the newly developed, first-of-its-kind compact X-ray light source (CXLS), which is currently in commissioning at Arizona State University. To assess the validity of the COC device, serial crystallography experiments were performed on the model protein lysozyme at the new European Synchrotron Radiation Facility-Extremely Brilliant Source (ESRF-EBS) beamline ID29. A 1.6 Å crystal structure of the protein was solved, demonstrating that, in general, the COC device can be used to generate high-quality data from macromolecular crystals at the CXLS and synchrotron radiation sources, which holds enormous potential for advancing the field of protein structure determination by fixed-target X-ray crystallography.

Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics

Proteins guide the flows of information, energy, and matter that make life possible by accelerating transport and chemical reactions, by allosterically modulating these reactions, and by forming dynamic supramolecular assemblies. In these roles, conformational change underlies functional transitions. Time-resolved X-ray diffraction methods characterize these transitions either by directly triggering sequences of functionally important motions or, more broadly, by capturing the motions of which proteins are capable. To date, most successful have been experiments in which conformational change is triggered in light-dependent proteins. In this review, I emphasize emerging techniques that probe the dynamic basis of function in proteins lacking natively light-dependent transitions and speculate about extensions and further possibilities. In addition, I review how the weaker and more distributed signals in these data push the limits of the capabilities of analytical methods. Taken together, these new methods are beginning to establish a powerful paradigm for the study of the physics of protein function.

Flow Chemistry: A Sustainable Voyage Through the Chemical Universe en Route to Smart Manufacturing

Microfluidic devices and systems have entered many areas of chemical engineering, and the rate of their adoption is only increasing. As we approach and adapt to the critical global challenges we face in the near future, it is important to consider the capabilities of flow chemistry and its applications in next-generation technologies for sustainability, energy production, and tailor-made specialty chemicals. We present the introduction of microfluidics into the fundamental unit operations of chemical engineering. We discuss the traits and advantages of microfluidic approaches to different reactive systems, both well-established and emerging, with a focus on the integration of modular microfluidic devices into high-efficiency experimental platforms for accelerated process optimization and intensified continuous manufacturing. Finally, we discuss the current state and new horizons in self-driven experimentation in flow chemistry for both intelligent exploration through the chemical universe and distributed manufacturing. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis

Room-temperature (RT) protein crystallography provides significant information to elucidate protein function under physiological conditions. In particular, contrary to typical binding assays, X-ray crystal structure analysis of a protein–ligand complex can determine the three-dimensional (3D) configuration of its binding site. This allows the development of effective drugs by structure-based and fragment-based (FBDD) drug design. However, RT crystallography and RT crystallography-based protein–ligand complex analyses require the preparation and measurement of numerous crystals to avoid the X-ray radiation damage. Thus, for the application of RT crystallography to protein–ligand complex analysis, the simultaneous preparation of protein–ligand complex crystals and sequential X-ray diffraction measurement remain challenging. Here, we report an RT crystallography technique using a microfluidic protein crystal array device for protein–ligand complex structure analysis. We demonstrate the microfluidic sorting of protein crystals into microwells without any complicated procedures and apparatus, whereby the sorted protein crystals are fixed into microwells and sequentially measured to collect X-ray diffraction data. This is followed by automatic data processing to calculate the 3D protein structure. The microfluidic device allows the high-throughput preparation of the protein–ligand complex solely by the replacement of the microchannel content with the required ligand solution. We determined eight trypsin–ligand complex structures for the proof of concept experiment and found differences in the ligand coordination of the corresponding RT and conventional cryogenic structures. This methodology can be applied to easily obtain more natural structures. Moreover, drug development by FBDD could be more effective using the proposed methodology.

Room temperature protein crystallography and its application to protein–ligand complex structure analysis was demonstrated using a microfluidic protein crystal array device.

In Meso In Situ Serial X-Ray Crystallography (IMISX): A Protocol for Membrane Protein Structure Determination at the Swiss Light Source

The lipid cubic phases (LCP) have enabled the determination of many important high-resolution structures of membrane proteins such as G-protein-coupled receptors, photosensitive proteins, enzymes, channels, and transporters. However, harvesting the crystals from the glass or plastic plates in which crystals grow is challenging. The in meso in situ serial X-ray crystallography (IMISX) method uses thin plastic windowed plates that minimize LCP crystal manipulation. The method, which is compatible with high-throughput in situ measurements, allows systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without direct crystal harvesting. In this chapter, we describe an IMISX protocol for in situ serial X-ray data collection of LCP-grown crystals at both cryogenic and room temperatures which includes the crystallization setup, sample delivery, automated serial diffraction data collection, and experimental phasing. We also detail how the IMISX method was applied successfully for the structure determination of two novel targets-the undecaprenyl-pyrophosphate phosphatase BacA and the chemokine G-protein-coupled receptor CCR2A.

A fixed-target platform for serial femtosecond crystallography in a hydrated environment

For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering.

Application of electric fields for controlling crystallization

This highlight gives a helicopter view on the application of electric fields and discusses its potential future applications.

A review on application of graphene‐based microfluidics

This review reports on the progress of recent developments in graphene‐based microfluidics. The applications of graphene‐based microfluidics that are the focus of this work are illustrated and discussed mainly with examples from detection of viruses and disease, detection of proteins and glucose, detection of contaminants, and applications in sensors and material preparation. A variety of microfluidic devices integrated with graphene are expounded and analysed. This paper will provide an expedient and valuable reference to designers researching graphene‐based microfluidics for various applications. © 2018 Society of Chemical Industry